Lord Coe, chairman of the London 2012 organisers, has admitted that the Olympics ticketing process is "not perfect". Photograph: Ian Nicholson/PA

London 2012 organisers will this week contact an estimated 90,000 successful applicants for Olympic tickets who have been unable to complete their orders because they do not have enough money in their accounts or have had their credit or debit cards stolen.

Amid frustration from some consumers over the ticket sales process, it has also emerged that there could be as many as one million applicants who got nothing at all in the first round of applications and so will be offered the first chance to apply for those remaining in the second phase.

Typically around 5% of ticket applicants have subsequent problems with lack of funds or lost and stolen cards. That would equate to around 90,000 2012 ticket applicants, although the numbers could be higher due to the sums involved and the uncertainty surrounding how much money would be deducted from bank accounts and credit cards and when.

The London Organising Committee of the Olympic Games and Paralympic Games has maintained that it has been as fair and transparent as possible in allocating the 6.6m tickets available to the British public in the face of criticism from consumer groups including Which? and some applicants who feel the balance was tilted in favour of those who could afford to risk large sums. There was also criticism of the fact that Locog deducted money from the accounts of successful applicants before notifying which specific tickets they had been allocated.

A total of 1.8m households applied for 20m tickets but it is believed that more than half those will end up with nothing at all. The majority of applications were for the same high-profile events at low prices, leading to huge over-demand for track cycling, the ceremonies and evening sessions in the pool and the main stadium.

Organisers, who point out that more than 2.5m tickets were available at £20 or less and highlight the fact that they have succeeded in selling out tickets for less high-profile sports such as rhythmic gymnastics as well as the expected big hits, will offer those who got nothing in the ballot first opportunity to apply for what is left next month.

Locog's chairman, Lord Coe, has admitted the system was "not perfect" and "was always going to be a challenge". "There is no perfect system. There is no ticket process on a scale like this, this is extraordinary," Coe said. There are expected to be large numbers of higher-value tickets left, particularly in team sports taking place in bigger venues with lots of sessions.

Organisers have yet to reveal when successful applicants will be told which tickets they have got, only that they will do so before 24 June. The vast majority of successful applicants saw money deducted by 31 May, leaving only those with problem cards or insufficient funds outstanding. Locog has resolved to get in touch with all of those applicants in order to try to resolve their issues. But if they are unable to do so, those tickets will be reallocated, meaning that some other applicants could see a second deduction from their account before Friday.